Variation that occurs in pathogens is based firmly upon one of three prime mechanisms of genetic variability: point mutations, genetic rearrangements, or lateral gene transfer (LGT). As LGT recently has been the focus of significant new insights into pathogen evolution it will be highlighted in this chapter. The intensive sequencing of microbial genomes and the comparisons made among them expanded our understanding of the scope of LGT in bacterial gene evolution. The main distinction is that the environment and ecology of pathogens is played out within another living organism-the host. The pan-genome represents the most accessible set of building blocks available for use in LGT. In the current environment, however, the widespread selective adaptation has spread because antibiotics are added to everything from cutting boards to cattle feed. The discussion of pathogenic gene content, style, and core distribution is intimately linked to the problem of defining both the species in bacteria and the events most likely to lead to new speciation. Multilocus sequence typing (MLST) involves the sampling of DNA sequences for a subset of housekeeping genes and the assessing of alleles for the purpose of studying the extent of recombination. LGT can cause shifts in the immediate pathogenesis of a clonally evolving group such as the clonal complex. The chapter reviews the way in which LGT has been an architect in the virulence, the genes, the genome, and the pan-genome of pathogens.

The pan-genome. The set of all genes within all members of a species is known as the pan-genome. It contains core genes and noncore genes. The noncore for the species is larger than shown here and bigger than the core. Within the core are sets of genes that are shared with the strain, the species, the genus, and all bacteria (hard core).

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Figure 1.

The pan-genome. The set of all genes within all members of a species is known as the pan-genome. It contains core genes and noncore genes. The noncore for the species is larger than shown here and bigger than the core. Within the core are sets of genes that are shared with the strain, the species, the genus, and all bacteria (hard core).